3DLR

Crystal structure of the catalytic core domain from PFV integrase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CXUPDB ENTRY 1cxu

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52911.0 M ammonium formate, 0.2 M magnesium cloride, 5 mM dithiotreitol, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0840.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.14α = 90
b = 52.14β = 90
c = 239.78γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-01-26MSINGLE WAVELENGTH
21x-rayCCDMARMOSAIC 225 mm CCD2008-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95373ESRFBM14
2SYNCHROTRONESRF BEAMLINE BM140.97837ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,22.245.1899.50.10517.48.9105841058432.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.3299.30.6813.49.31477

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTPDB ENTRY 1cxu2.245.189540104299.20.213940.209050.25922RANDOM32.046
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.820.410.82-1.23
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_2_deg35.371
f_dihedral_angle_4_deg16.931
f_dihedral_angle_3_deg16.041
f_dihedral_angle_1_deg5.838
f_scangle_it2.472
f_scbond_it1.746
f_angle_refined_deg1.122
f_mcangle_it1.025
f_mcbond_it0.558
f_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_2_deg35.371
f_dihedral_angle_4_deg16.931
f_dihedral_angle_3_deg16.041
f_dihedral_angle_1_deg5.838
f_scangle_it2.472
f_scbond_it1.746
f_angle_refined_deg1.122
f_mcangle_it1.025
f_mcbond_it0.558
f_nbtor_refined0.307
f_nbd_refined0.197
f_symmetry_vdw_refined0.149
f_symmetry_hbond_refined0.131
f_xyhbond_nbd_refined0.114
f_metal_ion_refined0.099
f_chiral_restr0.073
f_bond_refined_d0.01
f_gen_planes_refined0.004
f_bond_other_d
f_angle_other_deg
f_gen_planes_other
f_nbd_other
f_nbtor_other
f_xyhbond_nbd_other
f_metal_ion_other
f_symmetry_vdw_other
f_symmetry_hbond_other
f_symmetry_metal_ion_refined
f_symmetry_metal_ion_other
f_mcbond_other
f_rigid_bond_restr
f_sphericity_free
f_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1241
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement